Superhelical DNAs (FI DNAs) have special properties that may be utilized in important biological reactions. FI DNAs that are sufficiently supercoiled appear to contain regions of single-stranded character which renders such DNAs accessible to single-strand-specific reagents and endonucleases. The free energy associated with superhelix formation can be utilized to drive ligand or protein-DNA interactions. One or the other or both of these properties may be involved in the integration of bacterial viral DNA; more efficient transcription of FI DNA relative to relaxed (FII) or linear (FIII) DNA; recA-promoted recombination in E. coli; homologous uptake of single-stranded DNA and RNA fragments; and the opening of a particular region of the DNA for site specific conversion by an endonuclease. We have focused our attention on the role supercoiling plays in promoting enhanced transcription. Two systems are under investigation in our laboratory. We have examined the binding of E. coli RNA polymerase to SV40 and Co1 E1 DNAs by a variety of techniques. Extremely limited modification of SV40 DNA using a water soluble carbodiimide produces a significant loss of RNA polymerase binding as visualized by electron microscopy. Transcription is reduced by 61 and 88% in absence and presence of rifampin. Consequently chemical modification is highly selective in finding E. coli RNA polymerase promoters in superhelical DNA. The analysis of promoters in Col El DNA by filter binding, electron microscopy and sequence techniques will now permit us to extend our chemical modification studies using the above plasmid. Comparative analysis of promoter sensitivity in superhelical DNA should permit us to understand how supercoiling modulates gene expression and possibly other biological processes.